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FireRed/LeafGreen, EASILY. They went out of their way in those games to show how they relate to the Johto games 3 years later. >.> I don't see how any others COULD be considered "canon" over it.
For the most part, though, they're all canon minus minor inconsistencies that got corrected in later games and the odd mistake or two (the names of the Karate King and Janine in FRLG, for instance). FireRed/LeafGreen are remakes of Red/Green, not an alternate telling of the same rough storyline.
Either way, I don't know why you'd think Generation 1 would have been 100% correct in hindsight. I'm not even sure they were thinking of creating another set of games after Red/Green, let alone thinking of how to tie them together.
There's at least one NPC in Black/White or Black/White2 who points out that there are parallel universes in which things are just a wee bit different compared to the one you're playing in at that moment. That would also explain why a boy from Nuvema Town, who is Cheren's and Bianca's best friend and just set out with hem on a journey to beat the Elite Four and Team Plasma, can trade pokémon with hundreds of boys and girls from Nuvema Town, who just set out with the same Cheren and Bianca on the same journey to beat the Elite Four and Team Plasma, as well as thousands of other boys and girls from Nuvema Town who did the exact same thing over the past two years, together with their best friends, Cheren and Bianca.
As far as I'm concerned all of the main games are canon, in their own parallel universe. Even Yellow. :-p
3DS FC 4511-0567-3041 Martijn - inofficial pesky Claw using git of Kid Icarus Uprising's online modes